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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5714 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-02-22 22:34:43 +00:00
parent faf9b4f21b
commit f50885fd46
31 changed files with 0 additions and 40376 deletions
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2
examples/USER/eff/CH4/README
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Methane, valence electron ionization and full molecule tests (spe, min, dynamics).
Note: electron mass set to 1

32
examples/USER/eff/CH4/data.ch4
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Created by AJB
15 atoms
3 atom types
-500.0 500.0 xlo xhi
-500.0 500.0 ylo yhi
-500.0 500.0 zlo zhi
Masses
1 12.01070 # C nuclei mass
2 1.000794 # H nuclei mass
3 1.000000 # electron mass
Atoms
#id|type|q|spin|eradius|x|y|z|
1 1 6.0 0 0.0 0.0 0.0 0.0
2 2 1.0 0 0.0 1.0 1.0 1.0
3 2 1.0 0 0.0 -1.0 -1.0 1.0
4 2 1.0 0 0.0 1.0 -1.0 -1.0
5 2 1.0 0 0.0 -1.0 1.0 -1.0
6 3 0.0 -1 0.5 0.0 0.0 0.0
7 3 0.0 -1 1.0 1.0 1.0 1.0
8 3 0.0 -1 1.0 -1.0 -1.0 1.0
9 3 0.0 -1 1.0 1.0 -1.0 -1.0
10 3 0.0 -1 1.0 -1.0 1.0 -1.0
11 3 0.0 1 0.5 0.0 0.0 0.0
12 3 0.0 1 1.0 1.0 1.0 1.0
13 3 0.0 1 1.0 -1.0 -1.0 1.0
14 3 0.0 1 1.0 1.0 -1.0 -1.0
15 3 0.0 1 1.0 -1.0 1.0 -1.0

31
examples/USER/eff/CH4/data.ch4_ionized
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Created by AJB
14 atoms
3 atom types
-5000.0 5000.0 xlo xhi
-5000.0 5000.0 ylo yhi
-5000.0 5000.0 zlo zhi
Masses
1 12.01070 # C nuclei mass
2 1.000794 # H nuclei mass
3 1.000000 # electron mass
Atoms
1 1 6.000000 0 0.0 0.000000 -0.000000 0.000000
2 2 1.000000 0 0.0 1.247211 1.247211 1.247211
3 2 1.000000 0 0.0 -1.247211 -1.247211 1.247211
4 2 1.000000 0 0.0 1.247211 -1.247211 -1.247211
5 2 1.000000 0 0.0 -1.247211 1.247211 -1.247211
6 3 0.000000 -1 0.329128 -0.000000 0.000000 -0.000000
7 3 0.000000 -1 1.486181 0.979221 0.979221 0.979221
8 3 0.000000 -1 1.486181 -0.979221 -0.979221 0.979221
9 3 0.000000 -1 1.486181 0.979221 -0.979221 -0.979221
10 3 0.000000 -1 1.486181 -0.979221 0.979221 -0.979221
11 3 0.000000 1 0.329128 -0.000000 0.000000 0.000000
12 3 0.000000 1 1.486181 -0.979221 -0.979221 0.979221
13 3 0.000000 1 1.486181 0.979221 -0.979221 -0.979221
14 3 0.000000 1 1.486181 -0.979221 0.979221 -0.979221

40
examples/USER/eff/CH4/in.ch4.dynamics
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variable sname index ch4
log ${sname}.nve.log
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
pair_style eff/cut 100.0
pair_coeff * *
communicate single vel yes
# Minimize
min_style cg
dump 1 all custom 1 ${sname}.min.lammpstrj id type q spin eradius x y z
min_modify line quadratic dmax 0.1
minimize 0 1.0e-6 1000 10000
# Dynamics
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp press
thermo_modify temp effTemp
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
timestep 0.005
fix 1 all nve/eff
# the custom dump includes the radii
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q spin eradius x y z
dump 3 all xyz 1000 ${sname}.nve.xyz
run 100000

41
examples/USER/eff/CH4/in.ch4_ionized.dynamics
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variable sname index ch4_ionized
log ${sname}.nvt.log
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
pair_style eff/cut 5000.0 0 0
pair_coeff * *
communicate single vel yes
# minimize
min_style cg
min_modify line quadratic
minimize 0 1.0e-6 10000 100000
# dynamics
compute effTemp all temp/eff
thermo 100
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
# equilibrate
timestep 0.001
fix 1 all nvt/eff temp 300.0 300.0 0.1
# the custom dump includes the radii
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z spin eradius
dump 2 all xyz 100 ${sname}.nvt.xyz
run 1000000
fix 2 all nve/eff
run 1000000